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C

CABAminoAcidGenerator - Class in ProGAL.proteins.structure.generators

CABAminoAcidGenerator() - Constructor for class ProGAL.proteins.structure.generators.CABAminoAcidGenerator

calcRoots() - Method in class ProGAL.math.Polynomial

Find the roots of the polynomial.

calcRoots(double[]) - Static method in class ProGAL.math.Polynomial

Find the roots of the polynomial specified by the parameters.

calcRoots(double, double, double) - Static method in class ProGAL.math.Polynomial

Find the roots of a second degree polynomial.

calcRoots(double, double, double, double) - Static method in class ProGAL.math.Polynomial

Find the roots of a third degree polynomial.

CALoopStructure - Class in ProGAL.proteins.beltaStructure.loop

CALoopStructure(SecondaryStructure, int, int) - Constructor for class ProGAL.proteins.beltaStructure.loop.CALoopStructure

CALoopStructure.SegmentStructure - Class in ProGAL.proteins.beltaStructure.loop

Camera - Class in ProGAL.geom3d.viewer

Represents a camera located somewhere in the scene.

CanonicalSheet - Class in ProGAL.proteins.beltaStructure

CanonicalSheet(SheetTopology) - Constructor for class ProGAL.proteins.beltaStructure.CanonicalSheet

capWithDiscs(PointList) - Method in class ProGAL.geom3d.volumes.InfCylinder

capWithHalfSpheres(PointList) - Method in class ProGAL.geom3d.volumes.InfCylinder

capWithHalfSpheres(LSS, LSS) - Method in class ProGAL.geom3d.volumes.InfCylinder

CARTOON - Static variable in class ProGAL.proteins.viewer.PDBFileViewer

CBond - Class in ProGAL.proteins.structure

CBond(Atom, Atom) - Constructor for class ProGAL.proteins.structure.CBond

CEdge - Class in ProGAL.geom3d.complex

CEdge(CVertex, CVertex) - Constructor for class ProGAL.geom3d.complex.CEdge

cellFromPoint(Point) - Method in class ProGAL.dataStructures.rangeSearching.GridMap

center() - Method in class ProGAL.geom2d.Circle

center - Variable in class ProGAL.geom3d.Rectangle

centerCamera() - Method in class ProGAL.geom2d.viewer.J2DScene

Center the view on the objects in the scene

centerCamera() - Method in class ProGAL.geom3d.viewer.J3DScene

Sets the location that the camera looks at to the center of all the shapes added to the scene.

centerCamera(Point) - Method in class ProGAL.geom3d.viewer.J3DScene

chain - Variable in class ProGAL.proteins.PDBFile.AtomRecord

A character identifying the chain

chain - Variable in class ProGAL.proteins.PDBFile.TerRecord

ChainTree - Class in ProGAL.proteins.chainTree

A chain tree representation of the structure of a protein sub-chain.

ChainTree(PrimaryStructure) - Constructor for class ProGAL.proteins.chainTree.ChainTree

Construct a chain tree representing the structure of the specified sequence.

ChainTree(PrimaryStructure, int, int) - Constructor for class ProGAL.proteins.chainTree.ChainTree

Construct a chain tree representing the structure of the residues in the specified interval.

ChainTreeLoop - Class in ProGAL.proteins.beltaStructure

ChainTreeLoop(SecondaryStructure, int, int) - Constructor for class ProGAL.proteins.beltaStructure.ChainTreeLoop

changeAlpha(double) - Method in class ProGAL.geom3d.complex.alphaComplex.Node

changeDeath(double) - Method in class ProGAL.geom3d.complex.alphaComplex.Node

checkTessels() - Method in class ProGAL.geomNd.complex.delaunayComplex.BowyerWatson

Checks that all tetrahedra comply with the Delaunay-criteria.

checkTetrahedra() - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplex

Checks that all tetrahedra comply with the Delaunay-criteria.

checkTetrahedra() - Method in class ProGAL.geom3d.complex.tessellation.DelaunayTessellation

Checks that all tetrahedra comply with the Delaunay-criteria.

Circle - Class in ProGAL.geom2d

Circle(Point, double) - Constructor for class ProGAL.geom2d.Circle

Construct a circle with the given center and radius.

Circle(Circle) - Constructor for class ProGAL.geom2d.Circle

Constructs a circle that is a copy of a given circle

Circle(Point, Point) - Constructor for class ProGAL.geom2d.Circle

Circle(Point, Point, Point) - Constructor for class ProGAL.geom2d.Circle

Creates circle through 3 given points.

Circle(Circle, Circle) - Constructor for class ProGAL.geom2d.Circle

Circle(Circle, Circle, Circle) - Constructor for class ProGAL.geom2d.Circle

Circle(Triangle) - Constructor for class ProGAL.geom2d.Circle

Circle - Class in ProGAL.geom3d

A circle in (x,y,z)-space represented by a center-point, a radius and a normal-vector.

Circle(Point, double, Vector) - Constructor for class ProGAL.geom3d.Circle

Circle(Point, Point, Vector) - Constructor for class ProGAL.geom3d.Circle

A circle with given center through a given point and with specified normal vector

Circle(Point, Point, Point) - Constructor for class ProGAL.geom3d.Circle

Circle in the plane through p0, p1, p2

circumcenter() - Method in class ProGAL.geom3d.Triangle

Return the circumcenter of the triangle.

circumCenter() - Method in class ProGAL.geom3d.volumes.Tetrahedron

Find the center of the circumscribing sphere.

circumradius(Point, Point, Point, Point) - Method in class ProGAL.geom3d.predicates.ExactJavaPredicates

circumradius(Tetrahedron) - Method in class ProGAL.geom3d.predicates.ExactJavaPredicates

circumradius(Point, Point, Point) - Method in class ProGAL.geom3d.predicates.ExactJavaPredicates

circumradius(Triangle) - Method in class ProGAL.geom3d.predicates.ExactJavaPredicates

circumradius(Point, Point, Point, Point) - Method in class ProGAL.geom3d.predicates.ExactNativePredicates

circumradius(Tetrahedron) - Method in class ProGAL.geom3d.predicates.ExactNativePredicates

circumradius(Point, Point, Point) - Method in class ProGAL.geom3d.predicates.ExactNativePredicates

circumradius(Triangle) - Method in class ProGAL.geom3d.predicates.ExactNativePredicates

circumradius(Point, Point, Point, Point) - Method in class ProGAL.geom3d.predicates.InexactJavaPredicates

circumradius(Tetrahedron) - Method in class ProGAL.geom3d.predicates.InexactJavaPredicates

circumradius(Point, Point, Point) - Method in class ProGAL.geom3d.predicates.InexactJavaPredicates

circumradius(Triangle) - Method in class ProGAL.geom3d.predicates.InexactJavaPredicates

circumradius(Point, Point, Point, Point) - Method in class ProGAL.geom3d.predicates.InexactRegularJavaPredicates

circumradius(Tetrahedron) - Method in class ProGAL.geom3d.predicates.InexactRegularJavaPredicates

circumradius(Point, Point, Point) - Method in class ProGAL.geom3d.predicates.InexactRegularJavaPredicates

circumradius(Triangle) - Method in class ProGAL.geom3d.predicates.InexactRegularJavaPredicates

circumradius(Point, Point, Point, Point) - Method in class ProGAL.geom3d.predicates.Predicates

circumradius(Tetrahedron) - Method in class ProGAL.geom3d.predicates.Predicates

circumradius(Point, Point, Point) - Method in class ProGAL.geom3d.predicates.Predicates

circumradius(Triangle) - Method in class ProGAL.geom3d.predicates.Predicates

circumradius() - Method in class ProGAL.geom3d.Triangle

Return the circumradius of the triangle.

circumRadius() - Method in class ProGAL.geom3d.volumes.Tetrahedron

Calculate the radius of the circumsphere.

circumSphere - Variable in class ProGAL.geom3d.tessellation.BowyerWatson.Tet

circumSphere() - Method in class ProGAL.geom3d.volumes.Tetrahedron

Find the circumscribing sphere

clear() - Method in class ProGAL.dataStructures.DLCyclicList.DLNode

Clears the node and returns its object

clear() - Method in class ProGAL.dataStructures.Heap

remove all elements

clear() - Method in class ProGAL.dataStructures.Set

click() - Method in interface ProGAL.dataStructures.viewer.InteractiveBinaryTree

click() - Method in class ProGAL.geom3d.complex.alphaComplex.Node

ClickListener - Interface in ProGAL.geom3d.viewer

clone() - Method in class ProGAL.geom2d.LineSegment

clone() - Method in class ProGAL.geom2d.LSC

clone() - Method in class ProGAL.geom2d.Point

clone() - Method in class ProGAL.geom2d.Vector

clone() - Method in class ProGAL.geom3d.LineSegment

Returns a deep clone of this line segment.

clone() - Method in class ProGAL.geom3d.Point

Return a new object that equals this object.

clone() - Method in class ProGAL.geom3d.PointList

Get a shallow copy of this list.

clone() - Method in class ProGAL.geom3d.surface.ParametricParaboloid

clone() - Method in class ProGAL.geom3d.surface.ParametricPlane

clone() - Method in class ProGAL.geom3d.surface.ParametricSurface

clone() - Method in class ProGAL.geom3d.Triangle

clone() - Method in class ProGAL.geom3d.Vector

Create a clone of this vector.

clone() - Method in class ProGAL.geom3d.volumes.Cone

clone() - Method in class ProGAL.geom3d.volumes.Cylinder

clone() - Method in class ProGAL.geom3d.volumes.Lens

clone() - Method in class ProGAL.geom3d.volumes.LSS

clone() - Method in class ProGAL.geom3d.volumes.OBB

clone() - Method in class ProGAL.geom3d.volumes.RSS

clone() - Method in class ProGAL.geom3d.volumes.Sphere

Returns a deep clone of this sphere.

clone() - Method in class ProGAL.geom3d.volumes.Tetrahedron

clone() - Method in interface ProGAL.geom3d.volumes.Volume

Make a deep clone this volume.

clone() - Method in class ProGAL.geomNd.Point

clone() - Method in class ProGAL.geomNd.PointList

Get a shallow copy of this list.

clone() - Method in class ProGAL.geomNd.Vector

Create a clone of this vector.

clone() - Method in class ProGAL.math.Matrix

Returns a clone of this matrix.

clone() - Method in class ProGAL.math.Matrix3x3

clone() - Method in class ProGAL.proteins.beltaStructure.sheet.ParametricSurface

clone() - Method in class ProGAL.proteins.structure.AminoAcid

clone() - Method in class ProGAL.proteins.structure.Atom

clone() - Method in class ProGAL.proteins.viewer.CoilSurface

clone() - Method in class ProGAL.proteins.viewer.HelixSurface

clone() - Method in class ProGAL.proteins.viewer.StrandSurface

closeCCD(Point[], int) - Method in class ProGAL.proteins.chainTree.ChainTree

Perform cyclic coordinate descent on this chain so the positions of the end-atoms overlap with those specified in the target-array.

closestSegmentPoint(Point, Point, Point, Point) - Static method in class ProGAL.geom3d.Rectangle

28HOps at most.

closestSegmentPoint(Point, Point, Point) - Static method in class ProGAL.geom3d.Rectangle

closestSegmentPoint(LSS) - Method in class ProGAL.geom3d.volumes.LSS

CN_ClashLowerBound - Class in ProGAL.proteins.beltaStructure.bnb.lowerBounds

CN_ClashLowerBound(double[]) - Constructor for class ProGAL.proteins.beltaStructure.bnb.lowerBounds.CN_ClashLowerBound

CoilDatabase - Class in ProGAL.proteins.beltaStructure.loop

CoilDatabase() - Constructor for class ProGAL.proteins.beltaStructure.loop.CoilDatabase

CoilSurface - Class in ProGAL.proteins.viewer

collinear(Point, Point, Point) - Static method in class ProGAL.geom2d.Point

collinear(Point, Point, Point) - Static method in class ProGAL.geom3d.Point

Returns true if three points are on the same line.

collinear(Point, Point, Point) - Static method in class ProGAL.geomNd.Point

Combinatorics - Class in ProGAL.math

A wrapper for static combinatorial helper functions.

Combinatorics() - Constructor for class ProGAL.math.Combinatorics

CombinatoricsTest - Class in ProGAL.math.test

CombinatoricsTest() - Constructor for class ProGAL.math.test.CombinatoricsTest

COMP_EQUAL - Static variable in interface ProGAL.dataStructures.SortTool

COMP_GRTR - Static variable in interface ProGAL.dataStructures.SortTool

COMP_LESS - Static variable in interface ProGAL.dataStructures.SortTool

compare(Point, Point) - Method in class ProGAL.dataStructures.rangeSearching.rangeTree.PointDimensionComparator

compare(Object, Object) - Method in interface ProGAL.dataStructures.SortTool

compare(Object, Object) - Method in class ProGAL.dataStructures.SortToolDouble

compare(Object, Object) - Method in class ProGAL.dataStructures.SortToolInteger

compare(Object, Object) - Method in class ProGAL.dataStructures.SortToolLineSegment2dAroundCommonPoint

compare(Object, Object) - Method in class ProGAL.dataStructures.SortToolLineSegment2dByLength

compare(Object, Object) - Method in class ProGAL.dataStructures.SortToolPoint2dAroundOrigo

compare(Object, Object) - Method in class ProGAL.dataStructures.SortToolPoint2dAroundPoint

compare(Object, Object) - Method in class ProGAL.dataStructures.SortToolPoint2dDistance

compare(Object, Object) - Method in class ProGAL.dataStructures.SortToolPoint2dXY

compare(Object, Object) - Method in class ProGAL.dataStructures.SortToolString

compare(Object, Object) - Method in class ProGAL.geom3d.complex.delaunayComplex.DelaunayComplexRotation.HeapItemComp

compareTo(BnBNode) - Method in class ProGAL.proteins.beltaStructure.bnb.BnBNode

cond() - Method in class ProGAL.math.SingularValueDecomposition

Two norm condition number

Cone - Class in ProGAL.geom3d.volumes

A three-dimensional cone represented by two points on its central axis.

Cone(Point, Point, double) - Constructor for class ProGAL.geom3d.volumes.Cone

Constants - Class in ProGAL.math

Constants() - Constructor for class ProGAL.math.Constants

Constraint - Interface in ProGAL.proteins.beltaStructure.bnb

contains(Object) - Method in class ProGAL.dataStructures.Set

contains(Point) - Method in class ProGAL.geom2d.Circle

contains(Circle) - Method in class ProGAL.geom2d.Circle

contains(Point) - Method in class ProGAL.geom2d.ConvexPolygon

returns true if point p is inside the convex polygon

contains(Point) - Method in class ProGAL.geom3d.Triangle

contains(Point) - Method in class ProGAL.geom3d.volumes.LSS

contains(Point) - Method in class ProGAL.geom3d.volumes.Sphere

Returns true if the given point is in the sphere.

contains(int) - Method in class ProGAL.proteins.belta.SecondaryStructure.SSSegment

containsBigPoint() - Method in class ProGAL.geom3d.complex.CTetrahedron

For computational convenience, the representation of a complex is based on a big tetrahedron that encloses all vertices.

containsBigPoint() - Method in class ProGAL.geom3d.complex.CTriangle

containsBigPoint() - Method in class ProGAL.geomNd.complex.Tessel

containsNone(List<Point>) - Method in class ProGAL.geom3d.volumes.Sphere

Returns true if none of the given points is in the sphere.

containsPoint(Point) - Method in class ProGAL.geom3d.complex.CEdge

containsPoint(CVertex) - Method in class ProGAL.geom3d.complex.CTetrahedron

containsPoint(CVertex) - Method in class ProGAL.geom3d.complex.CTriangle

containsPoint(Vertex) - Method in class ProGAL.geomNd.complex.Tessel

containsStrand(int) - Method in class ProGAL.proteins.belta.SheetTopology

Return true if the specified strand is in this sheet.

containsTriangle(CTriangle) - Method in class ProGAL.geom3d.complex.CTetrahedron

ConvexPolygon - Class in ProGAL.geom2d

ConvexPolygon() - Constructor for class ProGAL.geom2d.ConvexPolygon

ConvexPolygon(Polygon) - Constructor for class ProGAL.geom2d.ConvexPolygon

creates a convex hull of a simple polygon in O(n) time

ConvexPolygon(Point, Point, Point) - Constructor for class ProGAL.geom2d.ConvexPolygon

creates a convex polygon with given three points as corners (counterclockwise)

ConvexPolygon(PointSet, ConvexPolygon.ConvexHullAlgorithm) - Constructor for class ProGAL.geom2d.ConvexPolygon

creates a convex hull of a set of points Jarvis March O(hn) Grahams Scan O(nlogn)

ConvexPolygon.ConvexHullAlgorithm - Enum in ProGAL.geom2d

coords - Variable in class ProGAL.proteins.PDBFile.AtomRecord

coplanar(Point, Point, Point, Point) - Static method in class ProGAL.geom3d.Point

Returns true if four specified points are in the same plane

Corner - Class in ProGAL.geom3d.tessellation.BowyerWatson

Corner(Tet, PointWeighted) - Constructor for class ProGAL.geom3d.tessellation.BowyerWatson.Corner

cornerIdx(PointWeighted) - Method in class ProGAL.geom3d.tessellation.BowyerWatson.Tetr

Return the index of the specified corner-point and -1 if p is not a corner.

corners - Variable in class ProGAL.geom3d.tessellation.BowyerWatson.Tet

corners - Variable in class ProGAL.geom3d.tessellation.BowyerWatson.Tetr

cornerSides - Variable in class ProGAL.geom3d.tessellation.BowyerWatson.Tet

cornerSides[i] indicates the sign of orient(corners[i+1%4],corners[i+2%4],corners[i+3%4],corners[i]).

cornerSides - Variable in class ProGAL.geom3d.tessellation.BowyerWatson.Tetr

cornerSides[i] indicates the sign of orient(corners[i+1%4],corners[i+2%4],corners[i+3%4],corners[i]).

covalentBonds() - Method in class ProGAL.proteins.structure.AminoAcidChain

covalentBonds() - Method in class ProGAL.proteins.structure.Atom

create4x4ColumnMatrix(Vector, Vector, Vector, Vector) - Static method in class ProGAL.math.Matrix

createAndDrawDelaunay(List<Point>) - Static method in class ProGAL.geomNd.complex.delaunayComplex.BowyerWatson

Convenient static method for creating delaunay tessellation of a point-set and if its 2D or 3D also displaying it.

createBalancedHistogram(List<Double>, int) - Static method in class ProGAL.statistics.Histogram

Construct an IrregularHistogram with min-value and bin-widths such that each bin contains roughly the same number of values if the values are added.

createBoundingBox_Covariance(PointList) - Static method in class ProGAL.geom3d.volumes.OBB

createBoundingCylinder_CovarianceFit(PointList) - Static method in class ProGAL.geom3d.volumes.Cylinder

createBoundingLSS(PointList) - Static method in class ProGAL.geom3d.volumes.LSS

createBoundingLSS_covariance(PointList) - Static method in class ProGAL.geom3d.volumes.LSS

createBoundingLSS_MaxDist(LSS, LSS) - Static method in class ProGAL.geom3d.volumes.LSS

createBoundingRSS_covariance(PointList) - Static method in class ProGAL.geom3d.volumes.RSS

createBoundingRSS_covariance(RSS, RSS) - Static method in class ProGAL.geom3d.volumes.RSS

createBoxFromBases(Vector[], List<Point>) - Static method in class ProGAL.geom3d.volumes.OBB

Creates a bounding box enclosing the points in points using the supplied bases.

createColumnMatrix(Vector, Vector, Vector) - Static method in class ProGAL.math.Matrix

createControlPanel() - Method in class ProGAL.geom3d.viewer.Camera

createDelaunay(List<Point>) - Static method in class ProGAL.geomNd.complex.delaunayComplex.BowyerWatson

Convenient static method for creating delaunay tessellation of a point-set

createDiff(Vector, Vector) - Static method in class ProGAL.geom2d.Vector

createFromPDB(PDBFile, SheetTopology) - Static method in class ProGAL.proteins.beltaStructure.CanonicalSheet

createIdentityMatrix(int) - Static method in class ProGAL.math.Matrix

createJ2DSceneInFrame() - Static method in class ProGAL.geom2d.viewer.J2DScene

Create a frame containing a canvas, display it and return the J2DScene object shown in the frame.

createJ3DSceneInFrame() - Static method in class ProGAL.geom3d.viewer.J3DScene

Create a frame containing a canvas, display it and return the J3DScene object shown in the frame.

createMinRadCylinderFromDirection(PointList, Vector) - Static method in class ProGAL.geom3d.volumes.InfCylinder

Assumes dir is normalized

createRandomMatrix(int) - Static method in class ProGAL.math.Matrix

createRotatedVector(double) - Method in class ProGAL.geom2d.Vector

createRotationMatrix(double, Vector) - Static method in class ProGAL.math.Matrix

createRowMatrix(Vector, Vector, Vector) - Static method in class ProGAL.math.Matrix

createSum(Vector, Vector) - Static method in class ProGAL.geom2d.Vector

createTree(double) - Method in class ProGAL.geom3d.complex.alphaComplex.VoidTree

cross(Vector) - Method in class ProGAL.geom3d.Vector

Get the cross-product of this vector and v (without changing this object).

crossProduct(Vector, Vector) - Static method in class ProGAL.geom2d.Vector

crossThis(Vector) - Method in class ProGAL.geom3d.Vector

Get the cross-product of this vector and v and store the result in this vector (changes this object).

crossThis(Vector) - Method in class ProGAL.geom3d.Vector.ImmutableVector3d

CTetrahedron - Class in ProGAL.geom3d.complex

An extension of the normal Tetrahedron that is used in complexes.

CTetrahedron(CVertex, CVertex, CVertex, CVertex) - Constructor for class ProGAL.geom3d.complex.CTetrahedron

CTriangle - Class in ProGAL.geom3d.complex

CTriangle(CVertex, CVertex, CVertex, CTetrahedron, CTetrahedron) - Constructor for class ProGAL.geom3d.complex.CTriangle

curChainID - Variable in class ProGAL.proteins.PDBFile.SheetRecord

curResSeq - Variable in class ProGAL.proteins.PDBFile.SheetRecord

cutArealYZ() - Method in class ProGAL.geom3d.volumes.OBB

CVertex - Class in ProGAL.geom3d.complex

CVertex(Point) - Constructor for class ProGAL.geom3d.complex.CVertex

CVertex(Point, boolean) - Constructor for class ProGAL.geom3d.complex.CVertex

CVertex.DegenerateCase - Enum in ProGAL.geom3d.complex

Cylinder - Class in ProGAL.geom3d.volumes

Cylinder(Point, Point, double) - Constructor for class ProGAL.geom3d.volumes.Cylinder

Cylinder(LineSegment, double) - Constructor for class ProGAL.geom3d.volumes.Cylinder